From 0c7d1e732c28843e78d361c1317469f8af931281 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Mon, 7 May 2012 18:38:49 -0400
Subject: [PATCH] In function read_frame, corrected periodic cell size and
angles read when reading a dcd
Angles for cells with axis not along xyz should be handled carefully
as they might be wrong (couldn't find documentation for dcd format).
---
modules/io/src/mol/dcd_io.cc | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 deletions(-)
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index e5422bda6..15a290279 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -152,9 +152,23 @@ bool read_frame(std::istream& istream, const DCDHeader& header,
//if(skip_flag) istream.seekg(14*4,std::ios_base::cur);
if(skip_flag){
istream.read(dummy,sizeof(dummy));
- istream.read(reinterpret_cast<char*>(&cell_size[0]),sizeof(float)*3);
- istream.read(reinterpret_cast<char*>(&cell_angles[0]),sizeof(float)*3);
+ double x,y,z,a,b,c;
+ istream.read(reinterpret_cast<char*>(&x),sizeof(double));
+ istream.read(reinterpret_cast<char*>(&a),sizeof(double));
+ istream.read(reinterpret_cast<char*>(&y),sizeof(double));
+ istream.read(reinterpret_cast<char*>(&b),sizeof(double));
+ istream.read(reinterpret_cast<char*>(&c),sizeof(double));
+ istream.read(reinterpret_cast<char*>(&z),sizeof(double));
istream.read(dummy,sizeof(dummy));
+ cell_size[0]=x;
+ cell_size[1]=y;
+ cell_size[2]=z;
+ cell_angles[0]=acos(a);
+ cell_angles[1]=acos(b);
+ cell_angles[2]=acos(c);
+ if(a!=0.0||b!=0.0||c!=0.0){
+ LOG_ERROR("LoadCHARMMTraj: periodic cell not parallelepipedic, cell angles might be wrong, handle carefully")
+ }
}
// read each frame
--
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